ECA's Bioinformatics Handbook
Preface
1 Introduction
2 Eric’s Notes of what he might do
- 2.1 Table of topics
I Part I: Essential Computing Skills
3 Overview of Essential Computing Skills
4 Essential Unix/Linux Terminal Knowledge
5 Shell programming
6 Sed, awk, and regular expressions
- 6.1 awk
- 6.2 sed
7 Working on remote servers
8 High Performance Computing Clusters (HPCC’s)
II Part II: Reproducible Research Strategies
9 Introduction to Reproducible Research
10 Rstudio and Project-centered Organization
- 10.1 Organizing big projects
- 10.2 Using RStudio in workflows with remote computers and HPCCs
  - 10.2.1 Keeping an RStudio project “in sync” with GitHub
  - 10.2.2 Evaluating scripts line by line on a remote machine from within RStudio
11 Version control
12 A fast, furious overview of the tidyverse
13 Authoring reproducibly with Rmarkdown
14 Managing Workflows with Snakemake
III Part III: Bioinformatic Analyses
15 Overview of Bioinformatic Analyses
16 DNA Sequences and Sequencing
17 Bioinformatic file formats
18 Genome Assembly
19 Alignment of sequence data to a reference genome (and associated steps)
20 Variant calling
- 20.1 Genotype Likelihoods
- 20.2 GATK’s gVCF Workflow
21 Boneyard
22 Basic Handling of VCF files
23 Bioinformatics for RAD seq data with and without a reference genome
24 Processing amplicon sequencing data
25 Variant Annotation
26 Whole genome alignment strategies
- 26.1 Mapping of scaffolds to a closely related genome
- 26.2 Obtaining Ancestral States from an Outgroup Genome
27 An example full workflow from sequences to variants
IV Part IV: Analysis of Big Variant Data
28 Bioinformatic analysis on variant data
V Part V: Population Genomics
29 Topics in pop gen
References
Published with bookdown

Practical Computing and Bioinformatics for Conservation and Evolutionary Genomics

Chapter 21 Boneyard

Standard stuff here.

Big focus on parallelizing.